We don't have to tolerate people who make women feel unsafe and unwelcome in our (or any) industry.
You seem to be arguing the usual tired old thing: "but he's a genius and does such great work that we should tolerate the bad things he does". I really thought we'd started to move past that over the last few years.
Hand waving and quietly ignoring is the mark of tolerance. But one wonders exactly how polite society is. One certainly presumes the existence of both knights for justice and hot ladies in a nation of millions. What society are we talking about?
I don't expect MIT to be any more representative of society than the NFL. It is a magnet for extreme people who defer common sense and common acceptance in search of very particular goals. I wonder if we were to get rid of Stallman and replace him, deserving as he must be, for a bust in our Hall of Fame if our society could resist defaming his very image and existence.